I hope it is only a matter of transfer of normal vibration to your intercooler.
I've heard that 3TGTEU's have a tendency to sheer flywheel bolts. If they are starting to stretch i'd imagine you'd notice vibration (in neautral). Having a flywheel sheer off sounds pretty terrifying to me - I think you'd notice vibration then
As I recall you have forged pistons. Where these matched in weight to the factory pistons? Or did you get the crank rebalanced for the new pistons? If the later how much did it cost?